Contacts of the strand formed by residues 29 - 35 (chain B) in PDB entry 3AUI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TYR* 4.1 3.3 - - - -
24B ASN* 2.8 36.0 + - - +
27B ALA* 3.2 13.1 - - + +
28B GLY* 1.3 79.9 - - - +
30B ALA* 1.3 64.5 + - - +
31B GLN* 4.8 4.7 - - + +
52B LEU* 4.1 10.8 - - + -
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 4.7 3.4 - - + -
22B PHE 3.3 7.2 - - - -
23B TYR* 4.2 2.0 - - - +
29B ALA* 1.3 79.5 - - - +
31B GLN* 1.3 63.5 + - - +
48B ALA* 3.4 46.4 - - + +
51B ALA* 3.8 15.3 - - + -
52B LEU* 3.7 14.7 - - + +
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Residues in contact with GLN 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.2 7.4 - - - -
22B PHE* 2.8 57.9 + - + +
24B ASN* 2.7 39.4 + - + +
27B ALA* 3.6 18.4 - - - +
29B ALA* 4.8 5.5 + - + +
30B ALA* 1.3 78.2 - - - +
32B ALA* 1.3 64.7 + - - +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 4.0 16.6 - - + -
20B ARG 3.2 9.2 - - - +
21B TYR* 3.7 24.6 - - + +
22B PHE* 4.6 2.3 - - - -
31B GLN* 1.3 76.5 - - - +
33B PHE* 1.3 60.4 + - - +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 4.0 15.3 - - + -
10B TYR 3.7 30.7 - - - -
11B ALA* 4.6 1.6 - - + -
18B ILE 3.5 0.7 - - - +
19B ILE* 3.7 5.4 - - - -
20B ARG* 2.8 43.5 + - + +
21B TYR 3.5 30.3 - - - -
22B PHE* 3.6 27.4 - + + -
32B ALA* 1.3 76.0 - - - +
34B VAL* 1.3 71.7 + - - +
35B TYR* 3.9 14.1 - - + -
43B ASN 4.0 9.6 - - - -
44B ASN* 3.6 29.8 - - + -
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.4 25.1 - - - +
16B ALA 4.7 2.5 - - - +
17B ARG* 4.3 28.7 - - + +
18B ILE 3.6 5.4 - - - +
19B ILE* 4.4 16.8 - - + +
33B PHE* 1.3 79.6 - - - +
35B TYR* 1.3 61.5 + - - +
36B GLY 4.1 0.3 + - - -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B TYR 4.0 7.4 - - - -
11B ALA 3.4 15.9 - - - -
16B ALA 3.5 3.1 - - - +
18B ILE* 2.7 60.4 + - + +
20B ARG* 3.7 47.1 - - + -
33B PHE* 3.6 12.0 + - + -
34B VAL* 1.3 72.7 - - - +
36B GLY* 1.3 58.3 + - - +
37B GLY* 3.2 41.2 + - - -
38B VAL* 3.2 20.0 + - - -
39B ARG 3.7 0.9 + - - -
40B ALA* 3.2 37.8 + - + +
44B ASN* 3.6 9.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il